Table 2 Linkage disequilibrium overlap of cis-eQTL-SNPs with cis-meQTL-SNPs

From: Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus

Source

Hippocampal cis-eQTL-SNPs

Brain cis-eQTLsa

Number of “clumped” cis-eQTL-SNPs

362

7961

eQTL-SNPs overlapping meQTL-SNPs

201/10,890

2196/10,890

Mean (eQTL-SNPs overlapping control-SNPs)

30.0/10,890

606.7/10,890

s.d. (eQTL-SNPs overlapping control-SNPs)

5.09

22.29

Error for the mean

0.010

0.044

Average enrichment

6.70

3.62

Empirical P-value

<10−6

<10−6

  1. Overlapping SNPs of the cis-eQTL-SNPs and cis-meQTL-SNPs were identified by the linkage disequilibrium (LD) clumping procedure implemented in PLINK34 (SNP pair-wise r 2 > 0.25 within 1 Mb). Empirical P-values were derived on the basis of 1,000,000 simulated sets of LD-clumped control-SNPs (non-QTL-SNPs with FDR > 10%; LD clumping: SNP pair-wise r 2 < 0.25 within 250 kb with reference to the most significantly associated SNP) matched for allele frequency
  2. aBrain cis-eQTL-SNPs were obtained from a recent exon-level eQTL study from 10 adult brain regions18
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